Ambiguous sequences in public microbial genomes - Overview - (Item C)

Microbial reference sequences (archaea, bacteria, fungi, and protozoa from NCBI RefSeq database (20.12.2016)) were split into separate contigs at stretches of 10 Ns or more. Contigs and scaffolds below 10 kb (original and new as the result of split) were aligened against the non-redundant nucleotide collection (nt) database from NCBI using BLASTn with a minimal e-value of 1e-6. Hits with less than 70% query coverage where discarded from further analysis. Hits where assigned their corresponding genus level (e.g. Bradyrizobium for Bradyrizobium lablabi), and if a hit was already assigned to genus or higher level the level was not changed. The best hit for a query sequence was determined according to the bitscore. Query sequences with only hits within their respective genus where regarded as non-ambiguous. The remaining sequences were regarded as ambiguous and removed before building a Kraken and a microbial BLAST microbial reference database.

Reference

Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. Scientific Reports, doi:10.1038/s41598-018-22416-4.